After reloading a few times, I found one instance where the Eye on Kolodnor (sic?) didn't get its invulnerability updated. From my logging, it seeemed like the LongRangePlanning thread for the AI wasn't actually running. After some minutes though it eventually ran and the invulnerability got updated.

This isn't a bug with the External Invulnerability per se, but a threading weirdness, therefor a Chris problem.

If you reload this enough times and mess with it (pausing, changing speeds) in some random combination, you should be able to reproduce the problem.

In AI.cs::DoLongRangePlanning, you can change the bool externalInvulnerabilityDebug = false; to true to get some debug statements so you can see precisely when the thread runs